Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
MOTIVATION:Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current impl...
| Main Authors: | , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Oxford University Press (OUP)
2013
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| _version_ | 1826260970591223808 |
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| author | Anderson, JWJ Haas, PA Mathieson, L-A Volynkin, V Lyngsø, R Tataru, P Hein, J |
| author_facet | Anderson, JWJ Haas, PA Mathieson, L-A Volynkin, V Lyngsø, R Tataru, P Hein, J |
| author_sort | Anderson, JWJ |
| collection | OXFORD |
| description | MOTIVATION:Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions. RESULTS:We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models. |
| first_indexed | 2024-03-06T19:14:11Z |
| format | Journal article |
| id | oxford-uuid:17c7f78a-bcd1-4eaf-b485-ff2bf8a2b32b |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:14:11Z |
| publishDate | 2013 |
| publisher | Oxford University Press (OUP) |
| record_format | dspace |
| spelling | oxford-uuid:17c7f78a-bcd1-4eaf-b485-ff2bf8a2b32b2022-03-26T10:39:27ZOxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:17c7f78a-bcd1-4eaf-b485-ff2bf8a2b32bEnglishSymplectic ElementsOxford University Press (OUP)2013Anderson, JWJHaas, PAMathieson, L-AVolynkin, VLyngsø, RTataru, PHein, JMOTIVATION:Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions. RESULTS:We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models. |
| spellingShingle | Anderson, JWJ Haas, PA Mathieson, L-A Volynkin, V Lyngsø, R Tataru, P Hein, J Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_full | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_fullStr | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_full_unstemmed | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_short | Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. |
| title_sort | oxfold kinetic folding of rna using stochastic context free grammars and evolutionary information |
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